The killings on 2nd April 2015 by the Islamic terror group al-Shabaab at Garissa University in North Eastern province left 147 people dead and 104 others hurt.
The second anniversary is being marked on the campus - which reopened last autumn - and also at Moi University in Eldoret, where some survivors were sent to resume their studies.
A member of staff at Garissa University told the Christian organisation Open Doors: "The number of non-Muslim students willing to study in Garissa is very small."
"This is because fear remains high and Garissa is not considered safe. With the memorial day coming, many are looking anxious and worried."
Somali-based al-Shabaab militants have been known for crossing the porous border into Kenya and raiding towns or attacking buses.
Prayers and fond memories are what we have to remember our dearly departed #147 Students. My most heartfelt condolences. #GarissaUni2YrsOn
— NICHOLAS OSEKO TRUMP (@NICHONASRI) April 2, 2017
A local pastor told Open Doors: "Fear is gripping non-Muslims in Garissa as we near the second anniversary of the massacre because rumours are spreading that al-Shabaab are preparing to avenge their fallen brothers killed in the KDF attack.
"The church in this area remains the 'softest' target and Christians are calling for prayers."
News that 31 al-Shabaab fighters were recently killed in the Jubaland area of neighbouring Somalia has exacerbated an already tense atmosphere in Garissa.
Drought is also compounding the issue.
Kenya is ranked 18th on the World Watch List 2017 for places where persecution against Christians is worst.
Open Doors, which compiles the list, has warned that violence against Christians has risen for the third year in a row.